Microbial Community Analysis inside a Biooxidation Heap for Gold Recovery in Equador

2017 ◽  
Vol 262 ◽  
pp. 135-138 ◽  
Author(s):  
Carlos L. Aspiazu ◽  
Paulina Aguirre ◽  
Sabrina Hedrich ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Fine Fraction ◽  
Community Analysis ◽  
Gold Recovery ◽  
Microbial Community Analysis ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Probable Number ◽  
Cell Numbers ◽  
Cell Counts

In a mine owned by the company Orenas S.A. (Equador), a biooxidation process for gold recovery has been developed. Refractory gold ore was crushed, milled and 500 ton of flotation concentrate was agglomerated by coating a support rock. This was piled up on a liner and the biooxidation process in the heap of 35x25x6 m3 was run for approximately 150 days. The oxidized material was subsequently removed for further processing. An outcrop allowed for depth dependent sampling of altogether 36 samples at three sites over the complete depth of 6 m. The fine fraction was removed from the host rock and sent to the laboratory for analysis of the microbial community. The pH ranged between 2.2 and 2.9. Total cell counts determined via counting under a fluorescence microscope after SYBR Green staining indicated a high microbial colonialization of the heap in all depths between 106 to 109 cells per g concentrate, however the highest cell numbers were mainly found in the upper 50 cm. Most-probable-number determination of living, acidophilic iron (II)-oxidizers for one site also revealed a decrease of cell numbers with depth (between 104 to 108 cells per g concentrate). Further molecular analyses of the community composition based on extracted DNA and 16S rRNA gene analyses by TRFLP and qPCR revealed a complex archaeal and bacterial community within the heap. It can be stated that an active community of acidophiles runs the biooxidation process in all sampled parts of the heap.

scholarly journals Quantitative Microbial Community Analysis of Three Different Sulfidic Mine Tailing Dumps Generating Acid Mine Drainage

2008 ◽  
Vol 74 (16) ◽  
pp. 5211-5219 ◽  
Author(s):  
Dagmar Kock ◽  
Axel Schippers
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Analysis ◽  
Sybr Green ◽  
Microbial Community Analysis ◽  
Probable Number ◽  
Cell Numbers ◽  
Tailing Dumps ◽  
Sulfur Oxidizing ◽  
Card Fish

ABSTRACT The microbial communities of three different sulfidic and acidic mine waste tailing dumps located in Botswana, Germany, and Sweden were quantitatively analyzed using quantitative real-time PCR (Q-PCR), fluorescence in situ hybridization (FISH), catalyzed reporter deposition-FISH (CARD-FISH), Sybr green II direct counting, and the most probable number (MPN) cultivation technique. Depth profiles of cell numbers showed that the compositions of the microbial communities are greatly different at the three sites and also strongly varied between zones of oxidized and unoxidized tailings. Maximum cell numbers of up to 109 cells g−1 dry weight were determined in the pyrite or pyrrhotite oxidation zones, whereas cell numbers in unoxidized tailings were significantly lower. Bacteria dominated over Archaea and Eukarya at all tailing sites. The acidophilic Fe(II)- and/or sulfur-oxidizing Acidithiobacillus spp. dominated over the acidophilic Fe(II)-oxidizing Leptospirillum spp. among the Bacteria at two sites. The two genera were equally abundant at the third site. The acidophilic Fe(II)- and sulfur-oxidizing Sulfobacillus spp. were generally less abundant. The acidophilic Fe(III)-reducing Acidiphilium spp. could be found at only one site. The neutrophilic Fe(III)-reducing Geobacteraceae as well as the dsrA gene of sulfate reducers were quantifiable at all three sites. FISH analysis provided reliable data only for tailing zones with high microbial activity, whereas CARD-FISH, Q-PCR, Sybr green II staining, and MPN were suitable methods for a quantitative microbial community analysis of tailings in general.

scholarly journals Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

2013 ◽  
Vol 80 (1) ◽  
pp. 177-183 ◽  
Author(s):  
Lavane Kim ◽  
Eulyn Pagaling ◽  
Yi Y. Zuo ◽  
Tao Yan
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Bacterial Species ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Property Change ◽  
And Control ◽  
Start Ups

ABSTRACTThe impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected,BurkholderialesandRhodocyclalesof theBetaproteobacteriaclass were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes.

scholarly journals Temporal Changes in Archaeal Diversity and Chemistry in a Mid-Ocean Ridge Subseafloor Habitat

2002 ◽  
Vol 68 (4) ◽  
pp. 1585-1594 ◽  
Author(s):  
Julie A. Huber ◽  
David A. Butterfield ◽  
John A. Baross
Keyword(s):  
Microbial Community ◽  
Hydrothermal Systems ◽  
Community Diversity ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Archaeal Diversity ◽  
Free Living ◽  
Probable Number ◽  
Diffuse Flow ◽  
Group I

ABSTRACT The temporal variation in archaeal diversity in vent fluids from a midocean ridge subseafloor habitat was examined using PCR-amplified 16S rRNA gene sequence analysis and most-probable-number (MPN) cultivation techniques targeting hyperthermophiles. To determine how variations in temperature and chemical characteristics of subseafloor fluids affect the microbial communities, we performed molecular phylogenetic and chemical analyses on diffuse-flow vent fluids from one site shortly after a volcanic eruption in 1998 and again in 1999 and 2000. The archaeal population was divided into particle-attached (>3-μm-diameter cells) and free-living fractions to test the hypothesis that subseafloor microorganisms associated with active hydrothermal systems are adapted for a lifestyle that involves attachment to solid surfaces and formation of biofilms. To delineate between entrained seawater archaea and the indigenous subseafloor microbial community, a background seawater sample was also examined and found to consist only of Group I Crenarchaeota and Group II Euryarchaeota, both of which were also present in vent fluids. The indigenous subseafloor archaeal community consisted of clones related to both mesophilic and hyperthermophilic Methanococcales, as well as many uncultured Euryarchaeota, some of which have been identified in other vent environments. The particle-attached fraction consistently showed greater diversity than the free-living fraction. The fluid and MPN counts indicate that while culturable hyperthermophiles represent less than 1% of the total microbial community, the subseafloor at new eruption sites does support a hyperthermophilic microbial community. The temperature and chemical indicators of the degree of subseafloor mixing appear to be the most important environmental parameters affecting community diversity, and it is apparent that decreasing fluid temperatures correlated with increased entrainment of seawater, decreased concentrations of hydrothermal chemical species, and increased incidence of seawater archaeal sequences.

scholarly journals Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos) Shown with 16S rRNA Gene-Based Microbial Community Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Isamu Maeda ◽  
Mohammad Shohel Rana Siddiki ◽  
Tsutomu Nozawa-Takeda ◽  
Naoki Tsukahara ◽  
Yuri Tani ◽  
...  
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Pathogenic Bacteria ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Intestinal Microbiome ◽  
Rrna Gene ◽  
Jungle Crow ◽  
Corvus Macrorhynchos

Jungle Crows (Corvus macrorhynchos) prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous toEimeriasp., which belongs to the protozoan phylumApicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the generaCampylobacterandBrachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

scholarly journals Universal 16s rRNA Primers BD1 For Soil Microbial Community Analysis

2006 ◽  
Vol 4 (4) ◽  
pp. 32-37
Author(s):  
Elisaveta V Korostik ◽  
Alexander G Pinaev ◽  
Gulnar A Akhtemova ◽  
Evgeniy E Andronov
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Community Studies ◽  
Bacterial Isolates ◽  
16S Rrna Gene Sequences ◽  
Soil Microbial ◽  
16S Rrna Clone Library

New universal 16S rRNa primers were constructed and tested. These primers allow identifying correct taxonomic position of bacterial isolates and were shown to be useful in microbial community studies. The primers enable to detect the vast majority of unique 16S rRNa gene sequences. In the study 160 restriction types were found in 16S rRNa clone library (190 clones).

scholarly journals Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

2017 ◽  
Vol 83 (20) ◽  
Author(s):  
N. B. Justice ◽  
A. Sczesnak ◽  
T. C. Hazen ◽  
A. P. Arkin
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Interspecific Interactions ◽  
Relative Fitness ◽  
Most Probable Number ◽  
Rrna Gene ◽  
Community Structures ◽  
Probable Number ◽  
Environmental Selection ◽  
Organism Interactions

ABSTRACT A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA gene amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCE Through highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.

scholarly journals Comparison of 16S rRNA Gene Based Microbial Profiling Using Five Next-Generation Sequencers and Various Primers

2021 ◽  
Vol 12 ◽  
Author(s):  
Changwoo Park ◽  
Seung Bum Kim ◽  
Sang Ho Choi ◽  
Seil Kim
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Lactococcus Lactis ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Next Generation ◽  
Universal Primer ◽  
Mock Communities

Microbial community analysis based on the 16S rRNA-gene is used to investigate both beneficial and harmful microorganisms in various fields and environments. Recently, the next-generation sequencing (NGS) technology has enabled rapid and accurate microbial community analysis. Despite these advantages of NGS based metagenomics study, sample transport, storage conditions, amplification, library preparation kits, sequencing, and bioinformatics procedures can bias microbial community analysis results. In this study, eight mock communities were pooled from genomic DNA of Lactobacillus acidophilus KCTC 3164T, Limosilactobacillus fermentum KCTC 3112T, Lactobacillus gasseri KCTC 3163T, Lacticaseibacillus paracasei subsp. paracasei KCTC 3510T, Limosilactobacillus reuteri KCTC 3594T, Lactococcus lactis subsp. lactis KCTC 3769T, Bifidobacterium animalis subsp. lactis KCTC 5854T, and Bifidobacterium breve KCTC 3220T. The genomic DNAs were quantified by droplet digital PCR (ddPCR) and were mixed as mock communities. The mock communities were amplified with various 16S rRNA gene universal primer pairs and sequenced by MiSeq, IonTorrent, MGIseq-2000, Sequel II, and MinION NGS platforms. In a comparison of primer-dependent bias, the microbial profiles of V1-V2 and V3 regions were similar to the original ratio of the mock communities, while the microbial profiles of the V1-V3 region were relatively biased. In a comparison of platform-dependent bias, the sequence read from short-read platforms (MiSeq, IonTorrent, and MGIseq-2000) showed lower bias than that of long-read platforms (Sequel II and MinION). Meanwhile, the sequences read from Sequel II and MinION platforms were relatively biased in some mock communities. In the data of all NGS platforms and regions, L. acidophilus was greatly underrepresented while Lactococcus lactis subsp. lactis was generally overrepresented. In all samples of this study, the bias index (BI) was calculated and PCA was performed for comparison. The samples with biased relative abundance showed high BI values and were separated in the PCA results. In particular, analysis of regions rich in AT and GC poses problems for genome assembly, which can lead to sequencing bias. According to this comparative analysis, the development of reference material (RM) material has been proposed to calibrate the bias in microbiome analysis.

scholarly journals Molecular analysis of the microbial community structures in water-flooding petroleum reservoirs with different temperatures

2012 ◽  
Vol 9 (4) ◽  
pp. 5177-5203 ◽  
Author(s):  
L.-Y. Wang ◽  
R.-Y. Duan ◽  
J.-F. Liu ◽  
S.-Z. Yang ◽  
J.-D. Gu ◽  
...  
Keyword(s):  
Microbial Community ◽  
Volatile Fatty Acids ◽  
Petroleum Reservoirs ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Water Flooding ◽  
Rrna Gene ◽  
Community Structures ◽  
Microbial Community Structures ◽  
Different Temperatures

Abstract. Temperature is one of the most important environmental factors regulating the activity and determining the composition of the microbial community. Analysis of microbial communities from six water-flooding petroleum reservoirs at temperatures from 20 to 63 °C by 16S rRNA gene clone libraries indicates the presence of physiologically diverse and temperature-dependent microorganisms in these subterrestrial ecosystems. In high-temperature petroleum reservoirs, most of the archaeal sequences belong to the thermophilic archaea including the genera Thermococcus, Methanothermobacter and Thermoplasmatales, most of the bacterial sequences belong to the phyla Firmicutes, Thermotogae and Thermodesulfobacteria; in low-temperature petroleum reservoirs, most of the archaeal sequences are affiliated with the genera Methanobacterium, Methanoculleus and Methanocalculus, most of the bacterial sequences to the phyla Proteobacteria, Bacteroidetes and Actinobacteria. Canonical correspondence analysis (CCA) revealed that temperature, mineralization, ionic type as well as volatile fatty acids showed correlation with the microbial community structures. These organisms may be adapted to the environmental conditions of these petroleum reservoirs over geologic time by metabolizing buried organic matter from the original deep subsurface environment and became the common inhabitants in subsurface environments.

scholarly journals A New Approach To Utilize PCR–Single-Strand-Conformation Polymorphism for 16S rRNA Gene-Based Microbial Community Analysis

1998 ◽  
Vol 64 (12) ◽  
pp. 4870-4876 ◽  
Author(s):  
Frank Schwieger ◽  
Christoph C. Tebbe
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Pure Culture ◽  
Community Analysis ◽  
Single Strand Conformation Polymorphism ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Pcr Products ◽  
Conformation Polymorphism

ABSTRACT Single-strand-conformation polymorphism (SSCP) of DNA, a method widely used in mutation analysis, was adapted to the analysis and differentiation of cultivated pure-culture soil microorganisms and noncultivated rhizosphere microbial communities. A fragment (approximately 400 bp) of the bacterial 16S rRNA gene (V-4 and V-5 regions) was amplified by PCR with universal primers, with one primer phosphorylated at the 5′ end. The phosphorylated strands of the PCR products were selectively digested with lambda exonuclease, and the remaining strands were separated by electrophoresis with an MDE polyacrylamide gel, a matrix specifically optimized for SSCP purposes. By this means, reannealing and heteroduplex formation of DNA strands during electrophoresis could be excluded, and the number of bands per organism was reduced. PCR products from 10 of 11 different bacterial type strains tested could be differentiated from each other. With template mixtures consisting of pure-culture DNAs from 5 and 10 bacterial strains, most of the single strains could be detected from such model communities after PCR and SSCP analyses. Purified bands amplified from pure cultures and model communities extracted from gels could be reamplified by PCR, but by this process, additional products were also generated, as detected by further SSCP analysis. Profiles generated with DNAs of rhizosphere bacterial communities, directly extracted from two different plant species grown in the same field site, could be clearly distinguished. This study demonstrates the potential of the selected PCR–single-stranded DNA approach for microbial community analysis.

scholarly journals rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity

2000 ◽  
Vol 66 (8) ◽  
pp. 3376-3380 ◽  
Author(s):  
Ingela Dahllöf ◽  
Harriet Baillie ◽  
Staffan Kjelleberg
Keyword(s):  
Microbial Community ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rdna ◽  
Pattern Analysis ◽  
Community Analysis ◽  
Microbial Community Analysis ◽  
Rrna Gene ◽  
Community Pattern ◽  
16S Rdna Pcr

ABSTRACT Contemporary microbial community analysis frequently involves PCR-amplified sequences of the 16S rRNA gene (rDNA). However, this technology carries the inherent problem of heterogeneity between copies of the 16S rDNA in many species. As an alternative to 16S rDNA sequences in community analysis, we employed the gene for the RNA polymerase beta subunit (rpoB), which appears to exist in one copy only in bacteria. In the present study, the frequency of 16S rDNA heterogeneity in bacteria isolated from the marine environment was assessed using bacterial isolates from the red alga Delisea pulchra and from the surface of a marine rock. Ten strains commonly used in our laboratory were also assessed for the degree of heterogeneity between the copies of 16S rDNA and were used to illustrate the effect of this heterogeneity on microbial community pattern analysis. The rock isolates and the laboratory strains were also used to confirm nonheterogeneity of rpoB, as well as to investigate the versatility of the primers. In addition, a comparison between 16S rDNA and rpoB PCR-DGGE (denaturing gradient gel electrophoresis)-based community analyses was performed using a DNA mixture of nine isolates from D. pulchra. Eight out of 14 isolates from D. pulchra, all rock isolates, and 6 of 10 laboratory strains displayed multiple bands for 16S rDNA when analyzed by DGGE. There was no indication of heterogeneity for either the rock isolates or the laboratory strains when rpoB was used for PCR-DGGE analysis. Microbial community pattern analysis using 16S rDNA PCR-DGGE showed an overestimation of the number of laboratory strains in the sample, while some strains were not represented. Therefore, the 16S rDNA PCR-DGGE-based community analysis was proven to be severely limited by 16S rDNA heterogeneity. The mixture of isolates from D. pulchra proved to be more accurately described using rpoB, compared to the 16S rDNA-based PCR-DGGE.

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